Nuclear receptors (NRs) are one of the most important classes of regulatory molecules and major targets for pharmaceutical development. NRs are regulated by various small molecule ligands, acting as either agonists or antagonists. Such NR ligands account for about 20% of all pharmaceuticals and are used to treat conditions as diverse as diabetes, atherosclerosis, autoimmune disorders and cancer. Thyroid hormone (TH) receptors (TRs) regulate important processes involved in atherosclerosis, obesity and diabetes. Over the years, some of the most revealing discoveries in biology have come from determinations of atomic structures of large molecules. Our group has been determining atomic structures of TR ligand-binding domains (LBDs), using X- ray crystallography, and increasingly, other methods. This structural information, along with that obtained by others, has revealed multiple aspects of receptor function, and has helped to stimulate NR drug development within academia and the pharmaceutical/biotechnology industry. Selective TR agonists have shown great promise in animal trials for treating atherosclerosis, obesity and diabetes, and are now in human clinical trials. We have also made progress with TR and androgen receptor (AR) antagonist design to attack several problems, including those due to TH excess and drug resistance in cancer. We propose to obtain further insights through application of a variety of complementary structural approaches, including X-ray crystallography, hydrogen-deuterium exchange, molecular dynamics simulations, small angle X-ray solution scattering and nuclear magnetic resonance (NMR). We hope to understand variations in the active conformation in the hormone binding pocket and on the receptor surface, ligand effects on receptor conformation and function, mechanisms of selectivity in ligand binding and mechanisms of antagonist action. We will examine LBDs with native sequences or with natural mutations that occur in disease or artificial mutations that stabilize TRs. LBDs will either be bound to different agonists or antagonists with diverse structures (including small molecules that bind the TR surface) or unliganded with stabilizing partners, such as corepressor peptides and dimer/heterodimer partners. Since the LBD influences other receptor domains, and vice versa, and receptor activity is modulated by DNA binding we will also seek to understand these interactions by obtaining structural information about the TR LBD linked to its DNA-binding domain (DBD) or the full length receptor DNA. These structures will be analyzed with mutations, heterodimer partner and coregulator peptides as described above. Together, these studies should provide new insights into NR function in health and disease and will tell us how to devise strategies to modulate their function. Thyroid hormones elicit many actions that could be useful for treating/preventing atherosclerosis (including heart attack, stroke, kidney disease and peripheral vascular disease), obesity and diabetes, but also have undesirable effects. The proposed studies will help to better understand the receptors through which thyroid hormones work and should facilitate design of thyroid hormone like pharmaceuticals that have desired but not unwanted effects. The studies should also lead to principles that can be useful for developing pharmaceuticals that attack a number of other conditions.